Breast Cancer Area: Scientists with Datasets.    Github repository

Explore our interactive graph to see how breast cancer scientists work. Learn about their knowledge, the data they use, and the Bridge2AI scientists leading the way.

We use HetGNN (Heterogeneous Graph Neural Network) to represent node embeddings in the Breast Cancer area with the Pubmed Knowledge Graph Dataset. This includes four kinds of nodes: scientists, datasets, papers, and bioentities. Their relationships include writing, collaboration, mention, citing, and use.

We visualized scientists and datasets using K-means clustering (k=5) and T-SNE. The cluster labels are based on bioentities, abstracts, titles, TF-IDF, and chatGPT. At the bottom of this page, we list the main words of each cluster, including both bioentities-based and abstract-title-based clusters.

Operation Notes

  1. Use the mouse wheel or the ‘+’ and ‘-’ buttons on the top right of the canvas to zoom in and out.
  2. Hover over a node to see details.
  3. Double-click to autoscale and recover default settings.
  4. Click the legends to hide/show groups of nodes.
  5. Other tools are located on the top right of the canvas.

Cluster 0    Cancer signaling molecules (bioentities)   Therapeutic Mechanisms (keywords)

Bioentities: 'leptin', 'NF-κB', 'ATP', 'MAPK', 'DOX', 'AKT', 'MCF7', 'ERK', 'HBXIP', 'Bax', 'MTT', 'Bcl-2', 'oxygen', 'NF-B', 'CXCR4', 'STAT3', 'p38', 'anticancer', 'curcumin', 'siRNA', 'cisplatin', 'ERα', 'CSCs', 'mTOR', 'p21', 'PEG', 'PTX'

Keywords: 'rgd', 'western', 'anticancer', 'acid', 'investigated', 'apoptosis', 'integrin', 'mechanisms', 'enhanced', 'delivery', 'inhibits', 'nfb', 'present', 'line', 'demonstrated', 'induced', 'inhibit', 'antitumor', 'nanoparticles', 'therapeutic', 'mitochondrial', 'resistance', 'addition', 'drug', 'mechanism', 'assay', 'targeting'

Cluster 1    Health and disease risk factors (bioentities)   Epidemiology and Research Methods (keywords)

Bioentities: 'overweight', 'folate', 'colorectal cancer', 'insulin', 'BCS', 'postmenopausal breast cancer', 'Tamoxifen', 'testosterone', 'vitamin D', 'MD', 'depression', 'IGF-I', 'anxiety', 'prostate cancer', 'metformin', 'obesity', 'Participants', 'estrogens', '"breast', 'diabetes'

Keywords: 'confidence', 'la', 'rr', 'research', 'embase', 'incidence', 'casecontrol', 'polymorphism', 'science', 'population', 'ratio', 'cohort', 'screening', 'diagnosis', 'will', 'physical', 'care', 'interventions', 'de', 'models', 'published', 'mortality', 'health', 'searched', 'cochrane', 'web', 'intake', 'relationship', 'associations', 'age', 'subgroup', 'les', 'databases', 'odds', 'survivors', 'conducted', 'intervention'

Cluster 2    Breast cancer genetics and biomarkers (bioentities)   Genetics and Biomarkers (keywords)

Bioentities: 'ESR1', 'CHEK2', 'CBC', 'ATM', 'BRCA1 mutation', 'PRS', 'ERBB2', 'RNA', 'c', 'AR', 'PALB2', 'breast and ovarian cancer', 'BRCA2 mutations', 'miRNA', 'Estrogen', 'single nucleotide polymorphisms', 'TP53', 'familial breast cancer', 'FGFR2'

Keywords: 'brca2', 'network', 'brca1', 'variants', 'samples', 'mirnas', 'estrogen', 'mutation', 'identify', 'dna', 'differentially', 'functional', 'her2', 'biological', 'common', 'prognosis', 'status', 'er', 'independent', 'genes', 'interaction', 'database', 'impc', 'analyses', 'mutations'

Cluster 3    Breast cancer treatments (bioentities)   Cancer Treatment and Management (keywords)

Bioentities: '5-fluorouracil', 'early breast cancer', 'diarrhea', 'fulvestrant', 'SLN', 'pertuzumab', 'bevacizumab', 'taxanes', 'hormone receptor', 'G-CSF', 'palbociclib', 'CTC', 'zoledronic acid', 'everolimus', 'ABC', 'exemestane', 'gemcitabine', 'nausea', 'anthracyclines', 'methotrexate', 'neutropenia', 'vinorelbine', 'lapatinib', 'HER2-positive breast cancer', 'Trastuzumab', 'CMF', 'taxane', 'fluorouracil'

Keywords: 'apbi', 'radiation', 'followup', 'early', 'trial', 'time', 'median', 'patient', 'lesions', 'rate', 'hr', 'trastuzumab', 'adjuvant', 'radiotherapy', 'chemotherapy', 'treated', 'lymphedema', 'recurrence', 'outcome', 'reconstruction', 'only', 'sln', 'node', 'icg', 'neoadjuvant', 'efficacy', 'axillary', 'biopsy', 'advanced', 'os', 'rates', 'plus', 'surgery', 'toxicity', 'mastectomy', 'surgical', 'sentinel', 'randomized', 'months', 'fluorescence'

Cluster 4    Tumor microenvironment and metastasis molecules (bioentities)   Tumor Metastasis and Matrix Biology (keywords)

Bioentities: 'MMPs', 'MT1-MMP', 'TIMP-2', 'uPA', 'TIMP-1', 'carcinomas', 'collagen', 'uPAR', 'steroid', 'matrix metalloproteinases', 'tumor cell', 'MMP-1', 'MMP', 'PAI-1', 'carcinoma'

Keywords: 'carcinomas', 'suggest', 'metastases', 'metalloproteinase', 'serum', 'membrane', 'type', 'metalloproteinases', 'timp2', 'inhibitors', 'stromal', 'degradation', 'bone', 'mmps', 'timp1', 'mrna', 'mmp', 'mt1mmp', 'collagen', 'tumour', 'correlated', 'extracellular', 'mmp1'